annotate mzID_process2.py @ 80:6ad498eac0e2 draft default tip

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# -*- coding: utf-8 -*-
"""
Python-code: Preprocess mzIdentML
@author = Brent Kuenzi
@email = [e-mail]
"""
#######################################################################################
## Description: ##
#This program will create inter, prey, and bait files from mzIdentML files
## Required input: ##
# 1) mzIdentML file to be reformatted
# 2) minimum PSM for quantification


import sys
import os

ins_path = sys.argv[5]

class ReturnValue1(object):
	def __init__(self, sequence, gene):
		self.seqlength = sequence
		self.genename = gene
class ReturnValue2(object):
	def __init__(self, inter, accessions):
		self.inter = inter
		self.accessions = accessions
def read_tab(infile):
	with open(infile,'r') as x:
		output = []
		for line in x:
			line = line.strip()
			temp = line.split('\t')
			output.append(temp)
	return output
def printProgress (iteration, total, prefix = '', suffix = '', decimals = 1, barLength = 100):
	"""
	Call in a loop to create terminal progress bar
	@params:
		iteration   - Required  : current iteration (Int)
		total	   - Required  : total iterations (Int)
		prefix	  - Optional  : prefix string (Str)
		suffix	  - Optional  : suffix string (Str)
		decimals	- Optional  : positive number of decimals in percent complete (Int)
		barLength   - Optional  : character length of bar (Int)
	"""
	formatStr	   = "{0:." + str(decimals) + "f}"
	percents		= formatStr.format(100 * (iteration / float(total)))
	filledLength	= int(round(barLength * iteration / float(total)))
	bar			 = '=' * filledLength + '-' * (barLength - filledLength)
	sys.stdout.write('\r%s |%s| %s%s %s' % (prefix, bar, percents, '%', suffix)),
	sys.stdout.flush()
	if iteration == total:
		sys.stdout.write('\n')
		sys.stdout.flush()
def get_info(uniprot_accession_in,fasta_db): 
	# Get aminoacid lengths and gene name.
	error = open('error proteins.txt', 'a+')
	data = open(fasta_db, 'r')
	data_lines = data.readlines()
	db_len = len(data_lines)
	seqlength = 0
	count = 0
	last_line = data_lines[-1]
	for data_line in data_lines:
		if ">sp" in data_line:
			namer = data_line.split("|")[2]
			if uniprot_accession_in == data_line.split("|")[1]:
				match = count + 1
				if 'GN=' in data_line:
					lst = data_line.split('GN=')
					lst2 = lst[1].split(' ')
					genename = lst2[0]
				if 'GN=' not in data_line:
					genename = 'NA'
				while ">sp" not in data_lines[match]:
					if match <= db_len:
						seqlength = seqlength + len(data_lines[match].strip())
						if data_lines[match] == last_line:
							break
						match = match + 1
					else:
						break
				return ReturnValue1(seqlength, genename)
		if uniprot_accession_in == namer.split(" ")[0]:
			match = count + 1
			# Ensures consistent spacing throughout.
			if 'GN=' in data_line:
				lst = data_line.split('GN=')
				lst2 = lst[1].split(' ')
				genename = lst2[0]
			if 'GN=' not in data_line:
				genename = 'NA'
			while ">sp" not in data_lines[match]:
				if match <= db_len:
					seqlength = seqlength + len(data_lines[match].strip())
					if data_lines[match] == last_line:
						break
					match = match + 1
				else:
					break
			return ReturnValue1(seqlength, genename)
		count = count + 1
	if seqlength == 0:
		error.write(uniprot_accession_in + '\t' + "Uniprot not in Fasta" + '\n')
		error.close
		seqlength = 'NA'
		genename = 'NA'
		return ReturnValue1(seqlength, genename)
def make_inter(mzIdentML,replicate,grouping):
	accession_index = mzIdentML[0].index("accession")
	PSMs = {}
	accessions = []
	cnt = 0
	unique_lines = [mzIdentML[1:]]
	for i in mzIdentML[1:]:
		PSMs[i[accession_index]] = 0
		if i[accession_index] not in accessions:
			accessions.append(i[accession_index])
		if i not in unique_lines:
			unique_lines.append(i)
	for i in accessions:
		for j in unique_lines[1:]:
			if j[accession_index] == i:
				PSMs[j[accession_index]] +=1
	inter = ""
	for i in accessions:
		inter = inter + replicate + "\t" + grouping + "\t" + i + "\t" + str(PSMs[i]) + "\n"
	return ReturnValue2(inter,accessions)


files = sys.argv[1]
file_list = files.split(",")

make_prey = sys.argv[3]
db = sys.argv[4]
if db == "None":
	db = str(ins_path)  + "/SwissProt_HUMAN_2015_12.fasta"
make_bait = sys.argv[6]
bait_bool = sys.argv[7]
prey_file = sys.argv[8]
bait_out = sys.argv[9]
inter_out = sys.argv[10]

def bait_create(baits):
	# Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
	baits = make_bait.split()
	i = 0
	bait_file_tmp = open("bait.txt", "w")
	order = []
	bait_cache = []
	while i < len(baits):
		if baits[i+2] == "true":
			T_C = "C"
		else:
			T_C = "T"
		bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
		bait_cache.append(str(bait_line))
		i = i + 3

	for cache_line in bait_cache:
		bait_file_tmp.write(cache_line)

	bait_file_tmp.close()

if bait_bool == 'false':
	bait_create(make_bait, infile)
	bait = "bait.txt"
else:
	bait_temp_file = open(sys.argv[2], 'r')
	bait_cache = bait_temp_file.readlines()
	bait_file_tmp = open("bait.txt", "wr")
	for cache_line in bait_cache:
		bait_file_tmp.write(cache_line)
	bait_file_tmp.close()
	bait = "bait.txt"
bait = read_tab("bait.txt")

inter = ""
cnt = 0
accessions = []
for i in file_list:
	cmd = (r"Rscript "+ str(ins_path) +"flatten_mzIdentML.R " + i)
	os.system(cmd)
	mzIdentML = read_tab("flat_mzIdentML.txt")
	inter = inter + make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).inter
	accessions.append(make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).accessions)
	cnt+=1

with open("inter.txt","w") as x:
	x.write(inter)
if make_prey == "true":
	unique_accessions = []
	prey = ""
	for i in accessions:
		for j in i:
			if j not in unique_accessions:
				unique_accessions.append(j)
	start = 0
	end = len(unique_accessions)
	printProgress(start,end,prefix = "Making Prey File:",suffix = "Complete",barLength=50)

	for i in unique_accessions:
		prey = prey + i + "\t" + str(get_info(i,db).seqlength) + "\t" + get_info(i,db).genename + "\n"
		start+=1
		printProgress(start, end)
	with open("prey.txt","w") as x:
		x.write(prey)

os.rename("bait.txt", bait_out)
os.rename("inter.txt", inter_out)
if str(prey_file) != "None": 
	os.rename("prey.txt", prey_file)